I've lurked all over the internet looking at any request for help even similar to mine, 90% of them were silly admin errors, the rest had mod incompatibilities.

I have successfully used KSE in the past on multiple occasions with both Kotor I & II, though I don't know which version(right now 3.3.3), but for some reason it doesn't want to work for me. It opens up just fine, no error messages, running it in Admin(i do the same for Kotor I & II) I am able to edit just fine, also receiving no errors. I add feats no problem, they show up in game, I edit credits, light/dark, etc. not a single problem, but if I try to add Force Powers, it either adds some, but not all, none, or takes away powers I got in game. I am properly applying and committing(hence it working with everything else I do) and I have removed all of my mods. Any assistance would be much appreciated.

Is it possible that they were spells that your PC was not, level-wise, supposed to be able to get? This can cause problems, because the game has checks for such things, it references back and forth through scripted variables and their corresponding .2da... so if you aren't supposed to have a Force Power at the level you are, yet you DO have that power, the game might just freak out on you.

Same thing for Prestige class powers, if there are any ( :?: )

That's my only idea, but it seems to jive with my own memory of a similar experience.

I know this glitch, has happened to me.
Simply select all the powers you have AND ones you're going to add. (ctrl + click)
Hit remove powers, then add powers.
Finally commit changes, go into your game and you'll find all your powers and ones you added. (You can even give yourself lightsaber/force forms early on) (Follow these directions :3)

You have to do it like that or the force powers will keep fussing with you being all (I don't wanna be used :C)

Apparently there is a less painfully long process to this. Click the [+] next to Force Powers first before adding/removing powers so it doesn't break on you like that.http://www.lucasforums.com/showthread.php?t=194567
This method does not work, i tried it myself. ^

Which is why you check which ones you won't get on a specific playthrough.
Like if you're going to make a consular-master. Go ahead give yourself Niman - Juyo - Shien - Makashi - Ataru because the masters will only teach you force forms. You just have to be careful :3